Genome Analysis Wiki - User contributions [en]

Sean Caron

2024-05-15T17:06:35Z

Administrator:

[[Image:Sean_Caron_profile_5_2024.jpg|200px|right]]

Sean is responsible for the operation and maintenance of the Center's high performance computing cluster. She also provides end-user support to Center faculty, students and staff. Sean earned her B.S.E. in Electrical Engineering from the University of Michigan with a concentration in digital signal processing and control systems.
<P>
[http://github.com/seantcaron Sean's Github]

User:SCaron

2024-05-15T17:05:25Z

Administrator: Blanked the page

Sean Caron

2024-05-15T17:03:58Z

Administrator:

Abecasis Lab

2024-05-15T17:02:34Z

Administrator: /* Staff */

[[Image:AbecasisRetreat2016.jpg|700px|center|Group Photo 2016]]



== Mission Statement ==

We are developing and applying computational and statistical tools to further understanding of complex human diseases, such as cardiovascular disease and diabetes.

== Leadership ==

[[Goncalo Abecasis]] is currently the Felix Moore Collegiate Professor of Biostatistics at the University of Michigan School of Public Health.

== Current Members ==

=== Research Fellows ===

[[File:Kuser.png|50px]] Christian Fuchsberger

[[File:Sarah.jpg.jpg|50px]] Sarah Gagliano

[[File:PicJingjing.jpg|50px]] Jingjing Yang

=== Graduate Students ===

[[File:SaiChen.jpg|50px]] Sai Chen

[[File:Geng.jpg|50px]] Priscilla Geng

[[File:HeadOfAlanKwong.jpg|50px]] [[Alan Kwong]]

[[File:Kuser.png|50px]] Sebanti Sengupta

[[File:Headshot.jpg|50px]] Joshua Weinstock

[[File:Gregory3.jpg|50px]] Greg Zajac

[[File:Fan.jpg|50px]] Fan Zhang

[[File:Kuser.png|50px]] Wei Zhou

[[File:Xutong.jpg|50px]] Xutong Zhao

=== Staff ===

[[File:Irene_headshot.jpg|50px]] Irene Felicetti : Administrative Assistant Sr.

[[File:TomBlackwell_crop.jpg|50px]] [[Tom Blackwell]] : Research Area Specialist Sr.

[[File:Sean_Caron_profile_5_2024.jpg|50px]] [[Sean Caron]] : OS Programmer Lead

[[File:Headshot-chris-clark-2 (3).jpg|50px]] Chris Clark : Applications Programmer/Analyst Sr.

[[File:Kuser.png|50px]] Jonathon LeFaive : Applications Programmer/Analyst Sr.

[[File:Kevin_Web-Profile.jpg ‎|50px]] Kevin Li : Web Applications Developer

[[File:IMG_4735.JPG|50px]] Anita Pandit : Research Computer Specialist

[[File:Schmidt_small.jpg|50px]] Ellen Schmidt : Research Area Specialist Lead

[[File:pjvh.jpg|50px]] Peter VandeHaar : Applications Programmer/Analyst Sr.

[[File:MK_head.jpg|50px]] [[Mary Kate Wing]] : Applications Programmer working on GotCloud Pipelines, C++ library & tools (libStatGen, bamUtils)

== Alumni ==

=== Former Research Faculty ===

* Hyun Min Kang (''graduated in 2011''), now Assistant Professor at the [http://www.sph.umich.edu/biostat/ University of Michigan School of Public Health, Department of Biostatistics].

=== Former Research Fellows ===

* Weimin Chen (graduated 2007), now Associate Professor at the [http://people.virginia.edu/~wc9c/ Department of Public Health Sciences & Center for Public Health Genomics, University of Virginia]

* Goo Jun (graduated 2014), now Assistant Professor at the [https://scholar.google.com/citations?user=1wzhcEQAAAAJ&hl=en University of Texas Health Sciences Center]

* Bingshan Li (graudated 2011), now Assistant Professor at the [https://medschool.vanderbilt.edu/cqs/people/Bingshan/Li/cqs-faculty-members Center for Quantitative Sciences, Vanderbilt University]

* [[Dajiang Liu]] (graduated 2013), now Assistant Professor at the [http://www-personal.umich.edu/~dajiang/ Penn State University College of Medicine]

* Serena Sanna (graduated 2007), now an investigator at the [http://www.serenasanna.com/ Istituto di Neurogenetica e Neurofarmacologia in Sardinia, Italy]

* Paul Scheet (graduated 2008), now Associate Professor at [http://faculty.mdanderson.org/Paul_Scheet/Default.asp?SNID=221605974 Department of Epidemiology, University of Texas MD Anderson Cancer Center]

* Carlo Sidore (graduated 2012), now an investigator at the [http://www.cnr.it/istituti/DatiGenerali.html?cds=060 Istituto di Neurogenetica e Neurofarmacologia in Sardinia, Italy]

* Fabio Busonero (graduated 2012), now an investigator at the [http://www.cnr.it/istituti/DatiGenerali.html?cds=060 Istituto di Neurogenetica e Neurofarmacologia in Sardinia, Italy]

* William Stewart (graduated 2008), now Assistant Professor at [http://www.mathmed.org/#William_Stewart Battelle Center for Computational Medicine, Departments of Statistics and Pediatrics, National Children's Hospital and Ohio State University]

* Alex Tsoi (graduated 2014), now Research Assistant Professor at [https://www.med.umich.edu/DERM/faculty/alextsoi_pub.shtml University of Michigan Medical School]

* [[Scott Vrieze]] (graduated 2014), now an Assistant Professor of Psychology and Neuroscience at [http://www.colorado.edu/ibg/people/471 University of Colorado, Boulder]

* [[Lars Fritsche]] (graduated 2016), now an Associate Professor at [http://www.ntnu.edu/ism the Department of Public Health and General Practice at the Norwegian University of Science and Technology] in Trondheim, Norway

=== Former Doctoral Students ===

* Katharine Brieger, now Graduate Student, Epidemiology, School of Public Health, University of Michigan

* Wei Chen (graduated 2011), now Assistant Professor at the [http://www.chp.edu/CHP/Chen%2C+Wei%2C+PhD Department of Pediatrics, University of Pittsburgh Medical Center]

* Jun Ding (graduated 2010), now Staff Scientist / Facility Head at the [http://www.grc.nia.nih.gov/branches/lg/lg.htm Laboratory of Genetics, National Institute on Aging (NIH)].

* Shuang Feng (graduated 2015), now Senior Data Scientist at Uber.

* Weihua Guan (graduated 2010), now Assistant Professor at the [http://sph.umn.edu/faculty1/expertise/statistical-genetics/name/weihua-guan/ Department of Biostatistics, University of Minnesota School of Public Health].

* Yun Li (graduated 2009), now Assistant Professor at the [http://www.sph.unc.edu/?option=com_profiles&Itemid=6138&profileAction=ProfDetail&pid=708777879 Department of Biostatistics, University of North Carolina].

* Youna Hu (graduated 2012), now a Data Sciences Engineer at A9, a subsidiary of 23andMe, Inc.

* Mingyao Li (graduated 2005), now Associate Professor at the [http://www.cceb.upenn.edu/faculty/index.php?id=159 Department of Biostatistics and Epidemiology, University of Pennsylvania]

* Liming Liang (graduated 2009), now Associate Professor at the [http://www.hsph.harvard.edu/faculty/liming-liang/ Departments of Biostatistics and Epidemiology, Harvard University]

* Tasha Fingerlin (graduated 2003), now Associate Professor at the [http://www.ucdenver.edu/academics/colleges/PublicHealth/departments/Epidemiology/About/Faculty/Pages/FingerlinT.aspx Section of Epidemiology and Community Health, University of Colorado Health Sciences Center]

* Sara Rashkin (graduated 2015), now Post Doc at [http://wittelab.ucsf.edu/pages/people UCSF Witte Lab]

* Andrew Skol (graduated 2006), now Assistant Professor at the [http://med-www02.bsd.uchicago.edu/339/FacultyPro/faculty_profile.aspx?empl_id=10164 Section of Genetic Medicine, University of Chicago]

* [[Xiaowei Zhan]] (graduated 2014), now Assistant Professor at the [http://profiles.utsouthwestern.edu/profile/152189/xiaowei-zhan.html Department of Clinical Science, University of Texas - Southwestern Medical Center].

* Jin Zheng (graduated 2009), now working in the Pharmaceutical Industry at Eli Lilly.

=== Former Masters Students ===

* Su Chu

* Nate Cohen

* Melinda Curran

* Vesela Gateva

* Xijing Han

* Dan Hovelson

* Elizabeth Jewell

* Michelle Kleckner

* Ben Lerch

* Yanming Li

* Heather Munro

* Nick Seewald

* Theresa Scott (nee Daigneault)

* Matthew Snyder

* Vivian Wang

* Yuan Wei

* Abigail Woodroffe

* Zaojun Ye

* Matthew Zawitowski

* Anita Yu Zhao

* Wanlin Zheng

* Tingting Zhou

=== Former Staff ===

* Paul Anderson

* Laura Baker

* [[Jennifer Bragg-Gresham]]

* Johanna Forster

* Jan Wigginton

=== Visitors ===

* Qing Lu

* Andrea Maschio

* Giorgio Pistis

* Eleanora Porcu

* Toshiko Tanakato

== Really Useful Stuff ==

* [[Abecasis Group Awards]]
* [https://calendars.office.microsoft.com/pubcalstorage/m3n2kr0z1470909/Goncalo_Abecasis_Calendar(1).ics Goncalo's Calendar]

Sean Caron

2024-05-15T17:01:49Z

Administrator:

Sean Caron

2024-05-15T17:01:28Z

Administrator:

[[Image:Sean_Caron_profile_5_2024.jpg|200px|right]]

Sean is responsible for the operation and maintenance of the Center's high performance computing cluster. He also provides end-user support to Center faculty, students and staff. Sean earned his B.S.E. in Electrical Engineering from the University of Michigan with a concentration in digital signal processing and control systems.
<P>
[http://wildflower.diablonet.net/~scaron Sean's personal page]

File:Sean Caron profile 5 2024.jpg

2024-05-15T17:01:14Z

Administrator:

Abecasis Lab

2023-03-23T21:03:12Z

Administrator: Reverted edits by Sid666 (talk) to last revision by Goncalo

[[Image:AbecasisRetreat2016.jpg|700px|center|Group Photo 2016]]



== Mission Statement ==

We are developing and applying computational and statistical tools to further understanding of complex human diseases, such as cardiovascular disease and diabetes.

== Leadership ==

[[Goncalo Abecasis]] is currently the Felix Moore Collegiate Professor of Biostatistics at the University of Michigan School of Public Health.

== Current Members ==

=== Research Fellows ===

[[File:Kuser.png|50px]] Christian Fuchsberger

[[File:Sarah.jpg.jpg|50px]] Sarah Gagliano

[[File:PicJingjing.jpg|50px]] Jingjing Yang

=== Graduate Students ===

[[File:SaiChen.jpg|50px]] Sai Chen

[[File:Geng.jpg|50px]] Priscilla Geng

[[File:HeadOfAlanKwong.jpg|50px]] [[Alan Kwong]]

[[File:Kuser.png|50px]] Sebanti Sengupta

[[File:Headshot.jpg|50px]] Joshua Weinstock

[[File:Gregory3.jpg|50px]] Greg Zajac

[[File:Fan.jpg|50px]] Fan Zhang

[[File:Kuser.png|50px]] Wei Zhou

[[File:Xutong.jpg|50px]] Xutong Zhao

=== Staff ===

[[File:Irene_headshot.jpg|50px]] Irene Felicetti : Administrative Assistant Sr.

[[File:TomBlackwell_crop.jpg|50px]] [[Tom Blackwell]] : Research Area Specialist Sr.

[[File:Sean_head.jpg|50px]] [[Sean Caron]] : UNIX Systems Administrator

[[File:Headshot-chris-clark-2 (3).jpg|50px]] Chris Clark : Applications Programmer/Analyst Sr.

[[File:Kuser.png|50px]] Jonathon LeFaive : Applications Programmer/Analyst Sr.

[[File:Kevin_Web-Profile.jpg ‎|50px]] Kevin Li : Web Applications Developer

[[File:IMG_4735.JPG|50px]] Anita Pandit : Research Computer Specialist

[[File:Schmidt_small.jpg|50px]] Ellen Schmidt : Research Area Specialist Lead

[[File:pjvh.jpg|50px]] Peter VandeHaar : Applications Programmer/Analyst Sr.

[[File:MK_head.jpg|50px]] [[Mary Kate Wing]] : Applications Programmer working on GotCloud Pipelines, C++ library & tools (libStatGen, bamUtils)

== Alumni ==

=== Former Research Faculty ===

* Hyun Min Kang (''graduated in 2011''), now Assistant Professor at the [http://www.sph.umich.edu/biostat/ University of Michigan School of Public Health, Department of Biostatistics].

=== Former Research Fellows ===

* Weimin Chen (graduated 2007), now Associate Professor at the [http://people.virginia.edu/~wc9c/ Department of Public Health Sciences & Center for Public Health Genomics, University of Virginia]

* Goo Jun (graduated 2014), now Assistant Professor at the [https://scholar.google.com/citations?user=1wzhcEQAAAAJ&hl=en University of Texas Health Sciences Center]

* Bingshan Li (graudated 2011), now Assistant Professor at the [https://medschool.vanderbilt.edu/cqs/people/Bingshan/Li/cqs-faculty-members Center for Quantitative Sciences, Vanderbilt University]

* [[Dajiang Liu]] (graduated 2013), now Assistant Professor at the [http://www-personal.umich.edu/~dajiang/ Penn State University College of Medicine]

* Serena Sanna (graduated 2007), now an investigator at the [http://www.serenasanna.com/ Istituto di Neurogenetica e Neurofarmacologia in Sardinia, Italy]

* Paul Scheet (graduated 2008), now Associate Professor at [http://faculty.mdanderson.org/Paul_Scheet/Default.asp?SNID=221605974 Department of Epidemiology, University of Texas MD Anderson Cancer Center]

* Carlo Sidore (graduated 2012), now an investigator at the [http://www.cnr.it/istituti/DatiGenerali.html?cds=060 Istituto di Neurogenetica e Neurofarmacologia in Sardinia, Italy]

* Fabio Busonero (graduated 2012), now an investigator at the [http://www.cnr.it/istituti/DatiGenerali.html?cds=060 Istituto di Neurogenetica e Neurofarmacologia in Sardinia, Italy]

* William Stewart (graduated 2008), now Assistant Professor at [http://www.mathmed.org/#William_Stewart Battelle Center for Computational Medicine, Departments of Statistics and Pediatrics, National Children's Hospital and Ohio State University]

* Alex Tsoi (graduated 2014), now Research Assistant Professor at [https://www.med.umich.edu/DERM/faculty/alextsoi_pub.shtml University of Michigan Medical School]

* [[Scott Vrieze]] (graduated 2014), now an Assistant Professor of Psychology and Neuroscience at [http://www.colorado.edu/ibg/people/471 University of Colorado, Boulder]

* [[Lars Fritsche]] (graduated 2016), now an Associate Professor at [http://www.ntnu.edu/ism the Department of Public Health and General Practice at the Norwegian University of Science and Technology] in Trondheim, Norway

=== Former Doctoral Students ===

* Katharine Brieger, now Graduate Student, Epidemiology, School of Public Health, University of Michigan

* Wei Chen (graduated 2011), now Assistant Professor at the [http://www.chp.edu/CHP/Chen%2C+Wei%2C+PhD Department of Pediatrics, University of Pittsburgh Medical Center]

* Jun Ding (graduated 2010), now Staff Scientist / Facility Head at the [http://www.grc.nia.nih.gov/branches/lg/lg.htm Laboratory of Genetics, National Institute on Aging (NIH)].

* Shuang Feng (graduated 2015), now Senior Data Scientist at Uber.

* Weihua Guan (graduated 2010), now Assistant Professor at the [http://sph.umn.edu/faculty1/expertise/statistical-genetics/name/weihua-guan/ Department of Biostatistics, University of Minnesota School of Public Health].

* Yun Li (graduated 2009), now Assistant Professor at the [http://www.sph.unc.edu/?option=com_profiles&Itemid=6138&profileAction=ProfDetail&pid=708777879 Department of Biostatistics, University of North Carolina].

* Youna Hu (graduated 2012), now a Data Sciences Engineer at A9, a subsidiary of 23andMe, Inc.

* Mingyao Li (graduated 2005), now Associate Professor at the [http://www.cceb.upenn.edu/faculty/index.php?id=159 Department of Biostatistics and Epidemiology, University of Pennsylvania]

* Liming Liang (graduated 2009), now Associate Professor at the [http://www.hsph.harvard.edu/faculty/liming-liang/ Departments of Biostatistics and Epidemiology, Harvard University]

* Tasha Fingerlin (graduated 2003), now Associate Professor at the [http://www.ucdenver.edu/academics/colleges/PublicHealth/departments/Epidemiology/About/Faculty/Pages/FingerlinT.aspx Section of Epidemiology and Community Health, University of Colorado Health Sciences Center]

* Sara Rashkin (graduated 2015), now Post Doc at [http://wittelab.ucsf.edu/pages/people UCSF Witte Lab]

* Andrew Skol (graduated 2006), now Assistant Professor at the [http://med-www02.bsd.uchicago.edu/339/FacultyPro/faculty_profile.aspx?empl_id=10164 Section of Genetic Medicine, University of Chicago]

* [[Xiaowei Zhan]] (graduated 2014), now Assistant Professor at the [http://profiles.utsouthwestern.edu/profile/152189/xiaowei-zhan.html Department of Clinical Science, University of Texas - Southwestern Medical Center].

* Jin Zheng (graduated 2009), now working in the Pharmaceutical Industry at Eli Lilly.

=== Former Masters Students ===

* Su Chu

* Nate Cohen

* Melinda Curran

* Vesela Gateva

* Xijing Han

* Dan Hovelson

* Elizabeth Jewell

* Michelle Kleckner

* Ben Lerch

* Yanming Li

* Heather Munro

* Nick Seewald

* Theresa Scott (nee Daigneault)

* Matthew Snyder

* Vivian Wang

* Yuan Wei

* Abigail Woodroffe

* Zaojun Ye

* Matthew Zawitowski

* Anita Yu Zhao

* Wanlin Zheng

* Tingting Zhou

=== Former Staff ===

* Paul Anderson

* Laura Baker

* [[Jennifer Bragg-Gresham]]

* Johanna Forster

* Jan Wigginton

=== Visitors ===

* Qing Lu

* Andrea Maschio

* Giorgio Pistis

* Eleanora Porcu

* Toshiko Tanakato

== Really Useful Stuff ==

* [[Abecasis Group Awards]]
* [https://calendars.office.microsoft.com/pubcalstorage/m3n2kr0z1470909/Goncalo_Abecasis_Calendar(1).ics Goncalo's Calendar]

Main Page

2023-03-23T20:06:05Z

Administrator: Reverted edits by LaneBurgoyne120 (talk) to last revision by Administrator

<div id="mf-mainpage">


{| style="width:100%; background:#fcfcfc; margin-top:1.2em; border:1px solid #ccc;"
|-
| style="width:100%; text-align:center; white-space:nowrap; color:#000;" | <div style="font-size:162%; border:none; margin:0; padding:.1em; color:#000;">Abecasis Group Wiki</div>
|}

[[Image:AbecasisRetreat2016.jpg|700px|center|Group Photo 2016]]






== Welcome! ==

Welcome to our wiki!

If you would like to contribute, [[Special:UserLogin|log-in]] or [[Special:RequestAccount|request an account]]. We recommend using your e-mail address or Michigan uniqname as your user id.

For basic instructions, see [http://en.wikipedia.org/wiki/Wikipedia:Tutorial the Wikipedia Tutorial].

== Sequence Analysis Tools ==

We are developing [[Software|software tools]] for the analysis of next generation sequence data.

These tools include:

#Variant Calling with [[GlfSingle]] and [[GlfMultiples]]
#Variant Calling and De Novo Mutation Detection in Families with [[Polymutt]]
#Variant Annotations using [[VcfCodingSnps]]
#Rare Variant Analysis using [[RvTests]]
#Rare Variant Association Analysis in family samples [[FamRvTest]]
#Quality control using [[C++ Executable: fastQValidator|FastQValidator]], [[VerifyBamID]], and [[BamValidator]]
#C++ APIs for sequence analsysis using [[C++ Library: libStatGen]]
#Meta-analysis of single variant or gene-level associations [[RAREMETAL-SOFTWARE]]
#Sequencing study design helper [[Rarefy]]
#Local ancestry inference (ancestry painting) using off-targeted sequence data [[SEQMIX]]
#Association Container Toolbox [[EPACTS]]
#Fast Genotype Imputation Tool : [[Minimac3]]

These tools and additional tools can be found on the [[Software]] page.

We are developing Genome/Sequencing Processing Pipelines for anyone to use: [[GotCloud]]

== High Level Tutorials ==

Some high-level tutorials on the analysis of next generation sequence data:

#[[Evaluating a Read Mapper on Simulated Data]]
#[[SNP Call Set Properties]]
#[[Generic Exome Analysis Plan]]

== Projects ==

[[NHLBI Informatics Resource|NHLBI Genome Sequencing Project]]

[[SardiNIA]] - The SardiNIA longitudinal study of aging.

[[EMADS|Exome Meta-analysis of Drinking and Smoking (EMADS)]]

[http://www.1000genomes.org The 1000 Genomes Project]

== Learn Genetics ==

Faculty in the group teach in a variety of formal and informal settings. [[Class Notes|Class notes]] and relevant discussion are archived here.

== General Resources ==

*[[Computer How-Tos]]
</div>

Main Page

2023-03-23T18:40:39Z

Administrator: Reverted edits by KarolSwope72 (talk) to last revision by Administrator

Main Page

2023-03-23T18:34:34Z

Administrator:

Main Page

2023-03-23T18:30:00Z

Administrator: Blanked the page